Workflow for UV orientation
You can make sure your UV's are rotated the way you expect by loading in a test texture before saving out the UV layout. 

Blender has some built in textures which you can load by going to Image> New Image in the header of the UV Image Editor while in Edit mode for the object you are unwrapping.

Choosing 'Color Grid' and pressing 'OK', will load in the test texture. 



From here you can edit the UV's in the Image Editor using the normal rotation, grab and scale shortcuts until the UV's are rotated the way you want.

Below, I selected the row of quads by hovering my cursor over them and pressing L to trigger 'Select Linked', then R to rotate the UV island.



You can remove the texture once the UV's are aligned correctly.